Hi Pengfei,
Thank you for your nice reply!
I had a try, but didn't get it.
1. To create As3+ library file, I added As3+ into atomic_ions.lib via tleap -s -f As.in.
2. I took the parameters you gave as 12-6 LJ parameters.
And added the Rmin/2 and epsilon into frcmod.ions234lm_126_spce file.
3. Added {"As3+" "As" "sp3" } into leaprc.water.spce file.
4. tleap -s -f As_leap.in > As_leap.out, ERROR occured.
In leap.log file:
FATAL: Atom .R<ARS 18>.A<As 1> does not have a type.
How to use the two parameters in a correct way?
Looking forward to receive your help.
Best wishes
Yuan Min
> -----原始邮件-----
> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> 发送时间: 2017-12-14 00:54:52 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib
>
> Hi Yuan,
>
> I have replied another email you sent to you about this issue. Hope it can solve your problem.
>
> Kind regards,
> Pengfei
>
> > On Dec 12, 2017, at 9:11 PM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
> >
> > Hi,
> >
> > I want to simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib.
> > Is there any way to deal with it?
> > The tutorial here doesn't work. http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.html
> >
> > Looking forward to hear your help.
> >
> > Best wishes
> > Yuan Min
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Dec 15 2017 - 06:30:04 PST
